Mr Khan, a firebrand nationalist, has promised to create millions of jobs and build world-class hospital and school systems in the mainly Muslim country of 208 million people.
In Friday's lower house vote, Khan garnered 176 votes to defeat Shehbaz Sharif from the outgoing Pakistan Muslim League-Nawaz (PML-N) party, who won 96 votes.
The swearing-in ceremony will take place on Saturday (August 18).
Khan's Pakistan Tehreek-e-Insaf (PTI), or Pakistan Movement for Justice, won most votes in Pakistan's July 25 general election.
Khan's election was only the second democratic transfer of power since Pakistan's 1947 independence, and came at a time when relations with on-off ally the United States are fraying over alleged Pakistani support for militants waging war in Afghanistan.
Pakistani lawmakers will vote for a new prime minister Friday, with World Cup cricket hero and election victor Imran Khan expected to become the nuclear-armed country's new leader-in-waiting after weeks of working to form a coalition. He drew comparisons between Pakistan's Prime Minister-elect and U.S. president Donald Trump. "We will hold you accountable for stealing votes" firmly said Sharif and continued his diatribe over systematic election rigging hurling accusations.
The result brings him one step closer to ending decades of rotating leadership between the PML-N and the PPP, punctuated by periods of military rule. The army and Khan have denied the claims.
It is expected to form a coalition government in powerful Punjab province, formerly a PML-N stronghold, in coming days.
Addressing the house amid a ruckus by PML-N members and cheering by PTI legislators, a charged Khan said: "I promise my nation today that we will bring the tabdeeli (change) that this nation was starving for".
Most pressing will be a looming economic crisis, with speculation that Pakistan will have to seek a bailout from the International Monetary Fund.